Contacts of the helix formed by residues 219 - 235 (chain B) in PDB entry 1K0Y
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B LYS 3.8 3.6 + - - -
218B VAL* 1.4 69.8 - - - +
220B VAL* 1.3 58.3 + - - +
221B ASP* 3.3 10.7 + - - +
222B GLU* 3.1 46.9 + - + +
223B VAL* 2.9 31.5 + - - +
317B HIS* 5.4 3.2 + - - +
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B TRP* 4.1 17.3 - - + +
218B VAL* 3.3 15.2 + - + +
219B ASN* 1.3 72.5 + - - +
221B ASP* 1.4 61.4 + - - +
223B VAL* 4.3 0.2 - - - +
224B GLY* 2.8 29.5 + - - -
265B LYS* 4.8 2.9 - - - +
268B LEU* 3.8 37.4 - - + +
269B GLY* 4.0 9.4 - - - +
272B SER* 4.0 18.6 - - - +
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Residues in contact with ASP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ASN* 3.3 7.8 + - - +
220B VAL* 1.4 79.2 - - - +
222B GLU* 1.4 58.3 + - - +
224B GLY* 3.4 1.0 + - - -
225B GLY* 3.1 24.9 + - - -
261B LYS 5.0 0.9 - - - +
265B LYS* 3.2 54.6 + - + +
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Residues in contact with GLU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ASN* 3.1 36.1 + - - +
221B ASP* 1.4 74.4 - - - +
223B VAL* 1.4 68.0 + - - +
225B GLY* 3.3 2.4 + - - -
226B GLU* 3.0 34.6 + - + +
317B HIS* 3.3 30.0 + - - -
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TRP* 5.3 0.4 - - + -
218B VAL* 3.9 22.2 - - + -
219B ASN 2.9 23.2 + - - +
220B VAL 4.3 0.7 - - - +
222B GLU* 1.4 84.6 - - - +
224B GLY* 1.4 57.1 + - - +
226B GLU* 3.6 6.3 - - - +
227B ALA* 2.9 28.4 + - - +
268B LEU* 4.2 8.7 - - + -
310B LEU* 3.7 27.6 - - + -
313B VAL* 3.9 19.1 - - + -
314B LEU* 4.5 7.9 - - + -
317B HIS* 4.8 16.2 - - + +
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Residues in contact with GLY 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B VAL 2.8 18.5 + - - -
221B ASP 3.8 0.9 - - - -
223B VAL* 1.4 77.4 - - - +
225B GLY* 1.4 61.2 + - - +
227B ALA* 4.0 1.3 - - - +
228B LEU* 3.1 20.1 + - - +
264B GLY* 3.4 33.1 - - - +
268B LEU* 3.5 16.4 - - - +
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Residues in contact with GLY 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ASP 3.1 14.4 + - - -
222B GLU 3.3 2.7 + - - -
224B GLY* 1.4 74.7 - - - +
226B GLU* 1.4 55.6 + - - +
228B LEU* 4.2 0.9 - - - +
229B GLY* 2.9 27.5 + - - -
255B MET* 4.6 3.7 - - - +
260B VAL* 4.5 4.7 - - - +
261B LYS* 4.3 29.6 - - - -
264B GLY* 4.1 4.6 - - - -
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PRO* 4.6 1.9 - - - +
222B GLU* 3.0 23.3 + - + +
223B VAL* 3.6 9.2 - - - +
225B GLY* 1.4 75.3 - - - +
227B ALA* 1.4 56.8 + - - +
230B ARG* 2.8 77.0 + - - +
255B MET* 3.5 21.0 - - + +
313B VAL* 3.4 21.8 - - + +
316B HIS* 5.5 2.7 + - - -
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B VAL 2.9 17.5 + - - +
224B GLY* 4.0 4.0 - - - +
226B GLU* 1.4 73.4 - - - +
228B LEU* 1.4 61.1 + - - +
230B ARG 3.4 0.2 + - - -
231B LEU* 2.9 25.8 + - - +
268B LEU* 5.1 5.2 - - + -
306B LEU* 4.0 17.5 - - + +
309B VAL* 3.4 11.3 - - + +
310B LEU* 4.3 25.8 - - + -
313B VAL* 4.1 14.3 - - + +
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B GLY 3.1 16.6 + - - +
225B GLY 4.3 1.1 - - - +
227B ALA* 1.4 77.1 - - - +
229B GLY* 1.4 62.6 + - - +
231B LEU* 3.2 25.1 + - + +
232B LEU* 3.1 29.8 + - + +
242B PHE* 4.8 14.6 - - + -
245B PHE* 5.4 0.9 - - + -
260B VAL* 3.7 18.4 - - + +
263B HIS* 3.4 35.0 - - + -
264B GLY* 3.6 20.9 - - - +
267B VAL* 5.1 5.6 - - + -
306B LEU* 4.4 14.5 - - + +
348B HEM 5.2 4.5 - - + -
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Residues in contact with GLY 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B GLY 2.9 18.9 + - - -
228B LEU* 1.4 77.3 - - - +
230B ARG* 1.4 56.6 + - - +
232B LEU 3.2 2.1 + - - -
233B VAL* 3.0 31.4 + - - +
254B VAL* 3.5 15.8 - - - +
255B MET* 3.5 19.5 - - - -
260B VAL* 3.9 8.6 - - - +
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Residues in contact with ARG 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PHE* 2.9 41.0 + - - -
118A THR* 3.5 3.8 + - - +
119A PRO* 3.7 32.2 - - + +
122A HIS* 3.2 41.0 + - + +
226B GLU* 2.8 51.8 + - - +
229B GLY* 1.4 71.2 - - - +
231B LEU* 1.4 57.2 + - - +
233B VAL* 4.3 6.3 - - - -
234B VAL* 2.7 39.0 + - + +
255B MET* 3.8 2.2 - - + -
309B VAL* 3.7 15.0 - - + -
313B VAL* 3.8 15.7 - - - +
316B HIS* 3.9 17.9 + - - -
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ALA 2.9 15.7 + - - +
228B LEU* 3.2 29.8 + - + +
230B ARG* 1.4 75.2 - - - +
232B LEU* 1.4 59.4 + - + +
235B TYR* 2.9 43.6 + - + +
238B THR* 3.6 18.8 - - + +
302B ASN 4.7 0.7 - - - +
305B LEU* 3.8 31.0 - - + +
306B LEU* 3.9 17.5 - - + +
309B VAL* 4.0 9.6 - - + +
348B HEM 3.9 35.7 - - + -
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LEU* 3.1 20.2 + - + +
229B GLY 3.2 5.6 + - - +
231B LEU* 1.4 82.5 - - + +
233B VAL* 1.4 59.8 + - - +
236B PRO* 3.4 10.6 - - - +
238B THR* 3.2 28.7 - - - +
239B GLN* 2.9 36.1 + - + +
242B PHE* 3.7 39.5 - - + -
245B PHE* 5.7 0.2 - - + -
248B LEU* 4.6 9.4 - - + -
254B VAL* 3.8 12.1 - - + -
260B VAL* 3.9 30.3 - - + -
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PRO* 3.9 29.8 - - + +
120A ALA* 4.8 0.4 - - - -
123A ALA* 4.3 10.4 - - + +
229B GLY 3.0 22.0 + - - +
230B ARG* 3.1 6.3 + - - +
232B LEU* 1.4 76.0 - - - +
234B VAL* 1.4 65.3 + - - +
236B PRO* 3.5 16.5 - - - +
239B GLN* 5.0 1.1 - - - +
251B PRO* 3.9 34.5 - - + +
254B VAL* 3.8 24.0 - - + -
255B MET* 4.3 7.4 - - - -
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PRO 4.1 5.8 - - - +
122A HIS* 3.8 37.7 - - + +
123A ALA* 3.9 27.1 - - + +
126A ASP* 3.8 9.4 - - + +
230B ARG* 2.7 25.7 + - + +
233B VAL* 1.4 74.4 - - + +
235B TYR* 1.4 80.8 + - + +
236B PRO* 3.4 1.5 - - - +
309B VAL* 5.3 0.7 - - + -
541C ARG* 3.0 49.2 + - - +
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Residues in contact with TYR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 5.1 3.8 - - - +
122A HIS* 5.3 1.5 + - - -
126A ASP* 2.8 34.9 + - - -
231B LEU* 2.9 30.4 + - + +
234B VAL* 1.4 90.7 - - + +
236B PRO* 1.3 57.2 - - - +
237B TRP* 3.2 36.3 - + + -
238B THR* 2.7 45.1 + - + -
305B LEU* 4.1 19.5 - - + -
308B ASN* 5.8 4.4 - - + +
309B VAL* 3.7 22.4 - - + -
541C ARG* 3.4 6.1 - - - -
801D CNO 3.7 30.9 + + + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il